-Beta release 0.1.13 (28 February, 2011)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Beta Release 0.1.15 (10 April, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Noteable changes:
+
+ * Allow to perform variant calling or to extract information in multiple
+ regions specified by a BED file (`samtools mpileup -l', `samtools view -L'
+ and `bcftools view -l').
+
+ * Added the `depth' command to samtools to compute the per-base depth with a
+ simpler interface. File `bam2depth.c', which implements this command, is the
+ recommended example on how to use the mpileup APIs.
+
+ * Estimate genotype frequencies with ML; perform chi^2 based Hardy-Weinberg
+ test using this estimate.
+
+ * For `samtools view', when `-R' is specified, drop read groups in the header
+ that are not contained in the specified file.
+
+ * For `samtools flagstat', separate QC-pass and QC-fail reads.
+
+ * Improved the command line help of `samtools mpileup' and `bcftools view'.
+
+ * Use a global variable to control the verbose level of samtools stderr
+ output. Nonetheless, it has not been full utilized.
+
+ * Fixed an issue in association test which may report false associations,
+ possibly due to floating point underflow.
+
+(0.1.15: 10 April 2011, r949:203)
+
+
+
+Beta release 0.1.14 (21 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This release implements a method for testing associations for case-control
+data. The method does not call genotypes but instead sums over all genotype
+configurations to compute a chi^2 based test statistics. It can be potentially
+applied to comparing a pair of samples (e.g. a tumor-normal pair), but this
+has not been evaluated on real data.
+
+Another new feature is to make X chromosome variant calls when female and male
+samples are both present. The user needs to provide a file indicating the
+ploidy of each sample (see also manual bcftools/bcftools.1).
+
+Other notable changes:
+
+ * Added `bcftools view -F' to parse BCF files generated by samtools r921 or
+ older which encodes PL in a different way.
+
+ * Changed the behavior of `bcftools view -s'. Now when a list of samples is
+ provided, the samples in the output will be reordered to match the ordering
+ in the sample list. This change is mainly designed for association test.
+
+ * Sped up `bcftools view -v' for target sequencing given thousands of samples.
+ Also added a new option `view -d' to skip loci where only a few samples are
+ covered by reads.
+
+ * Dropped HWE test. This feature has never been implemented properly. An EM
+ should be much better. To be implemented in future.
+
+ * Added the `cat' command to samtools. This command concatenate BAMs with
+ identical sequence dictionaries in an efficient way. Modified from bam_cat.c
+ written by Chris Saunders.
+
+ * Added `samtools view -1' to write BAMs at a low compression level but twice
+ faster to create. The `sort' command generates temporary files at a low
+ compression level as well.
+
+ * Added `samtools mpileup -6' to accept "BAM" with Illumina 1.3+ quality
+ strings (strictly speaking, such a file is not BAM).
+
+ * Added `samtools mpileup -L' to skip INDEL calling in regions with
+ excessively high coverage. Such regions dramatically slow down mpileup.
+
+ * Updated `misc/export2sam.pl', provided by Chris Saunders from Illumina Inc.
+
+(0.1.14: 21 March 2011, r933:170)
+
+
+
+Beta release 0.1.13 (1 March, 2011)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The most important though largely invisible modification is the change of the
order of genotypes in the PL VCF/BCF tag. This is to conform the upcoming VCF
Single Individual Haplotyping (SIH) is added as an experimental feature. It
originally aims to produce haploid consensus from fosmid pool sequencing, but
also works with short-read data. For short reads, phased blocks are usually too
-short to be useful in most applications, but phasing can be powerful for ruling
-out some SNPs close to INDELs and some of clustered spurious SNPs between copies
-of CNVs. On one data set, phasing based SNP calling is better in terms of both
-sensitivity and specificity than the standard methods.
+short to be useful in many applications, but they can help to rule out part of
+SNPs close to INDELs or between copies of CNVs.
Other notable changes in samtools:
- * Construct per-sample consensus to reduced the effect of nearby SNPs in INDEL
- calling. This may reduce the power, but improves specificity.
+ * Construct per-sample consensus to reduce the effect of nearby SNPs in INDEL
+ calling. This reduces the power but improves specificity.
* Improved sorting order checking in indexing. Now indexing is the preferred way
to check if a BAM is sorted.
* Added `mpileup -A' to allow to use reads in anomalous pairs in SNP calling.
- * Added `mpileup -m' to allow fine control of INDEL candidates.
+ * Added `mpileup -m' to allow fine control of the collection of INDEL candidates.
* Added `mpileup -S' to compute per-sample strand bias P-value.
* Fixed segfault in indel calling related to unmapped and refskip reads.
* Fixed an integer overflow in INDEL calling. This bug produces wrong INDEL
- genotypes for longer INDELs, typically over 10bp.
+ genotypes for longer short INDELs, typically over 10bp.
* Fixed a bug in tview on big-endian machines.
* Fixed a compiling error when the knetfile library is not used. Fixed a
library compiling error due to the lack of bam_nt16_nt4_table[] table.
+ Suppress a compiling warning related to the latest zlib.
Other notable changes in bcftools:
* Updated the BCF spec.
* Added the `FQ' VCF INFO field, which gives the phred-scaled probability
- of all samples being the samei (identical to the reference or all homozygous
+ of all samples being the same (identical to the reference or all homozygous
variants). Option `view -f' has been dropped.
* Implementated of "vcfutils.pl vcf2fq" to generate a consensus sequence
* Fixed a minor bug in Fisher's exact test; the results are rarely changed.
-(0.1.13: 28 February 2011, r926+130)
+(0.1.13: 1 March 2011, r926:134)
projects / samtools.git / blobdiff